The erasure and re-establishment of epigenetic marks (epigenetic reprogramming) is initiated in mammals during early pre-implantation development. Following fertilization, the paternal and maternal genomes are extensively modified and reset around the time of implantation, which is thought to be required to establish the totipotency of the newly formed embryo. The two main types of epigenetic modifications are DNA methylation and histone modifications, which work together to affect gene expression in a heritable manner (without altering DNA sequence) and influence chromatin structure (Lewis, J. D. et al. Cell 69, 905-914 (1992); Nan, X. et al. Nature 393, 386-389 (1998); Jones, P. L. et al. Nat Genet 19, 187-191 (1998)).
DNA methylation is mediated by a family of DNA methyltransferases (DNMTs) that catalyze the transfer of a methyl group to the 5′-position of cytosine residues within CpG dinucleotides usually resulting in effective gene silencing (Robert, M. F. et al. Nat Genet 33, 61-65 (2003)). Although global DNA methylation patterns in pre-implantation development have been documented in several species, the study of DNMT expression, particularly in early human embryos, is incomplete, with focus on just a few stages of pre-implantation development and/or particular DNMT family members (May, A. et al. Biol Reprod 80, 194-202 (2009); Golding, M. C. et al. Gene Expr Patterns 3, 551-558 (2003); Vassena, R. et al. Mol Reprod Dev 72, 430-436 (2005); Huntriss et al. Mol Reprod Dev 67, 323-336 (2004)).
Histone modifications include, but are not limited to, the phosphorylation of serine residues, acetylation of lysine residues and the methylation of either lysine or arginine residues, all of which are mediated by different histone-modifying enzymes and may affect biological outcome ((Latham et al. Nat Struct Mol Biol 14, 1017-1024 (2007)). While some studies have analyzed a subset of histone modifications in pre-implantation embryos from different species, data remains limited, especially in the human (Liu, H. et al. Development 131, 2269-2280 (2004); Torres-Padilla et al. Nature 445, 214-218 (2007); Qiao, J. et al. Fertil Steril 93, 1628-1636 (2010); Sarmento, O. F. et al. J Cell Sci 117, 4449-4459 (2004)).
Infertility is a common health problem that affects 10-15% of couples of reproductive-age. In the United States alone in the year 2006, approximately 140,000 cycles of in vitro fertilization (IVF) were performed. This resulted in the culture of more than a million embryos annually with variable, and often ill-defined, potential for implantation and development to term. The live birth rate, per cycle, following IVF was just 29%, while on average 30% of live births resulted in multiple gestations. Multiple gestations have well-documented adverse outcomes for both the mother and fetuses, such as miscarriage, pre-term birth, and low birth rate. Potential causes for failure of IVF are diverse; however, since the introduction of IVF in 1978, one of the major challenges has been to identify the embryos that are most suitable for transfer and most likely to result in term pregnancy.
Previous studies have demonstrated that more than half of human embryos are aneuploid, carrying an abnormal chromosome number, which contributes to the low efficiency of in vitro fertilization (IVF). Traditional methods of evaluating IVF embryos involve subjective assessment of static morphologic criteria. Although there is a relationship between static embryo morphology and ploidy, the correlation has been weak. Consequently, multiple embryos with variable implantation potential may be transferred, leading to both high rates of embryonic loss and increased frequency of multiple gestations with higher maternal and perinatal risks.
In an effort to improve IVF success, clinics are increasingly using preimplantation genetic screening (PGS) in combination with growth to blastocyst stage to assist in selection of euploid embryos for transfer. However, extended culture of embryos may induce epigenetic changes during early embryogenesis, the long-term effects of which may be detrimental to offspring (Katari et al., Hum Mol Genet 2009 and others). In addition, the majority of data derived on human embryo development, by necessity is limited to that obtained from infertility clinics and embryos produced with germ cells that may be compromised. While such studies have proven to be invaluable, the interpretation of results and what should be considered “baseline” must be approached cautiously. Moreover, most studies of embryo development are conducted in the mouse or non-mammalian species, requiring extrapolation of results to human development. However, given extensive species-specific differences, even comparison between closely related mammalian species may be difficult. Thus, markers that can be identified and utilized or restored earliest in development with evidence of similar indications in fertile couples are of great clinical interest.